|
| Status |
Public on Sep 29, 2014 |
| Title |
EC_H3K4ME3_TNF_JQ1 |
| Sample type |
SRA |
| |
|
| Source name |
HUVEC
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K4me3
antibody catalog number: ab8580
cell type: endothelium
agent: TNF alpha and JQ1
duration: 1 hour pretreatment with JQ1 followed by 1 hour TNF alpha treatment
|
| Treatment protocol |
Cells were stimulated with human TNFalpha (25 ng/mL, hr) in the presence or absence of JQ1 (500 nM, 1 hour pretreatment)
|
| Growth protocol |
M199 + 20% FBS + 0.1% heparin + 50 micrograms/mL endothelial cell growth factors (ECGF).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
endothelium stimulated with TNF alpha and JQ1
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
|
| |
|
| Submission date |
Jan 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE53998 |
NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers [ChIP-Seq] |
| GSE54000 |
NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers |
|
| Relations |
| BioSample |
SAMN02581482 |
| SRA |
SRX425261 |
